How to Fix Leaky Gut When You Have Hashimoto’s Disease

Steps on How to Fix Leaky Gut

by integrativethyroid

What is Leaky Gut?

Leaky gut is better known as intestinal permeability in the medical world. 70-80% of our immune system lies within the gut so gut health is extremely important. Your gut, or intestines, are protected by a barrier made up of tightly connected tissue (junctions) which help keep the food you eat, as well as toxins and bacteria you ingest, separate from your bloodstream. The role of the small intestine is to break down food, absorb nutrients from that food and get rid of the unnecessary stuff.

Leaky gut is the result when the thin protective layer of the gut gets compromised. Food and other particles are literally leaking out of your gut and into your bloodstream. This is not supposed to happen. When it does, the immune system gets activated and launches itself into battle mode to attack the invasive foreign particles. Those particles are meant to stay and be broken down in the digestive tract.  A deficiency in good gut bacteria plus the foreign bodies in the bloodstream can result in chronic inflammation and a host of diseases, like autoimmune disease.

In the case of leaky gut and Hashimoto’s disease, the activated immune system is attacking (developing antibodies) against the thyroid. In the case of Rheumatoid Arthritis, the activated immune system is attacking the joints. The underlying mechanism is the same in different autoimmune diseases, only the targeted body part or organ changes. That is why you must fix your gut, especially if you have autoimmune disease. Once you have one autoimmune disease, you are at much greater risk for developing others. Below we discuss how to fix leaky gut.

Leaky Gut and Hashimoto’s Disease

There is still debate about whether Hashimoto’s disease causes leaky gut or whether leaky gut is the cause of Hashimoto’s. But there is no question that the two are linked. In fact, some degree of leaky gut is present in anyone who has an autoimmune disease whether its Crohn’s, rheumatoid arthritis, multiple sclerosis, Parkinson’s and/or psoriasis just to name a few.

It is believed that low thyroid hormone, along with other culprits, can cause leaky gut which results in a viscous cycle as leaky gut worsens Hashimoto’s disease by building up the autoimmune attack on the thyroid. Nutrient deficiency also becomes a huge issue as the intestines’ ability to assimilate and absorb nutrients from foods is compromised. It is not uncommon to see deficiencies in the B-vitamins, selenium, zinc, iron, Vitamin A amongst others in people with Hashimoto’s Thyroiditis aka autoimmune thyroid disease. All of these are important for healthy thyroid function.

One Month Thyroid Recovery Program

What Causes Leaky Gut?

There are a few culprits but here are the main ones:

Gluten: No one wants to hear it, no one wants to admit it. But gluten blows holes in your gut lining. Does it happen to everyone? No. Because everyone’s body is different. But even if you are gluten sensitive, and not a celiac, gluten can wreak havoc on your system. Talk to any functional or integrative doctor and they will tell you going gluten free is the absolute first step if you have Hashimoto’s or any other autoimmune disease. If you need scientific evidence, read this. The study states that gluten is responsible for an increase in zonulin, an inflammatory protein that breaks up the tight junctions in our gut.

This next culprit also increases zonulin.

Pathogenic Bacteria and Gut Infections: There is good gut bacteria and there is bad gut bacteria. I am speaking here about bad gut bacteria which typically enters the body through the mouth. Bad bacteria are acquired through contaminated food and water, by coming into contact with feces of an infected person or from contact with animals or their environments. Touching the feces of another person is easier than you might think. An example is if they went to the bathroom and didn’t wash their hands and then touched something that you happen to touch later. Your hands now have that pathogenic bacteria on it.

This pathogenic bacteria can lead to gut infections or an overgrowth of bad bacteria in the gut, which leads to something called gut dysbiosis or SIBO, small intestine bacterial overgrowth. It is very common in people with Hashimoto’s disease. You can get tested for this but not all tests produce accurate results, sometimes a one time fecal test doesn’t do the job. You many need several tests or a comprehensive stool analysis.

Other Food: It is not just gluten that can be the cause of food induced leaky gut. Dairy is also a big culprit. Sugar and processed foods irritate and blow holes through the intestinal lining of the gut. Inflammatory fats like vegetable and seed oils irritate the gut. Avoid canola, corn, safflower, sunflower, peanut and cottonseed oils. Stick to cold pressed extra virgin olive oil, coconut oil and avocado oils.

how to fix leaky gut


This one is controversial but grains and legumes can be bad for the gut lining. Some docs will tell you to eat lentils and seeds for gut health. Others will tell you to avoid them as they contain lectins and phytates which irritate the gut and make digestion difficult. If your gut was healthy, grains and legumes wouldn’t be an issue. For me, it was. I always felt terrible after eating them. I did something called the Autoimmune Protocol which avoided gluten, dairy, corn, grains, legumes, seeds,soy, alcohol etc…. anything potentially inflammatory. After less than two months, my antibodies went to ZERO …. meaning my immune system was not attacking my thyroid tissue anymore!

Heavy Metals & Toxins: Heavy metals irritate the gut lining and also lead to inflammation of the gut lining, both are precursors to leaky gut syndrome. If those heavy metals get through the gut wall and into the bloodstream, the effects can be devastating… everything from mental health issues to autoimmune disease. Heavy metals also affect the composition of good bacteria in the gut. Sources of heavy metal exposure are fish high in mercury, dental fillings, high heat cooking in aluminum foil, old aluminum and teflon cookware, cosmetics, deodorant and medicines. Sources of other toxins are pesticides, BPA from plastic, etc. That seems like a long list but all are easily fixable except for the dental mercury fillings, you will need to see a specialist (not just a regular dentist) about having them removed.

You can find a list of my approved cosmetics and cookware on Amazon

Alcohol: I know, I know. The consumption of alcohol alters gut health for the worse. It inhibits breakdown of food, kills good gut bacteria and inflames the gut lining just to name a few. You should avoid it as much as possible if you truly want to heal. Alcohol also has a very detrimental effect on thyroid health. Read: Can I Drink Alcohol with Hashimoto’s Disease?

Antibiotics & OTC Medications: Yup, medicines blow holes through your gut lining. If you need it, you need it but think twice before you pop that ibuprofen or acetaminophen. And do you have a cold or a true bacterial infection? Do not take antibiotics if you do not truly need them. And if you do have a serious infection which requires an antibiotic, make sure you take a strong probiotic to repopulate the good bacteria that was killed off. There are enough studies showing how the microbiota of children can drastically change even after one round of antibiotics, leaving them more susceptible to developing leaky gut and disease later. Even C-section births can do this but that is a discussion for another time. (P.S. I am not blaming any Moms here, I was a C-section birth)

Stress: Last but not least, Stress. Do you know that leaky gut has been linked to causing depression and anxiety? What’s worse is that habitual stress over a long period of time can lead to the formation of leaky gut. Chronic stress leads to gastrointestinal disease through a variety of biochemical changes in the body. One example is stress increases cortisol which puts your body into fight or flight mode. Blood is directed toward the brain, muscles and limbs and away from digestion, it actually becomes suppressed. It also revs up the immune system and causes short term inflammation. The immune system then becomes suppressed after these cortisol spikes. With long term stress, that inflammation becomes chronic and immune system even more suppressed (which means it cannot fight off bad bacteria).  The result is leaky gut and onset of disease.

If you have made all the necessary positive changes in your healing journey (giving up inflammatory foods, taking the right supplements, stress management) and are still not feeling better, I would test for both gut infections and heavy metals as a hidden source of cause. Toxic mold in your home or work environment may also be a cause of leaky gut!

Signs of Leaky Gut

There are varying degrees of intestinal permeability aka leaky gut. Anything from eczema to allergies to full blown autoimmune disease can be a sign.

Leaky gut and Hashimoto's Disease

How to Fix Leaky Gut

How do you fix leaky gut when you have thyroid disease or Hashimoto’s? We take a cue from an alternative approach and use the 4 R’s of Functional Medicine. Remove, Replace, Repair, Reinoculate. But first, it is helpful to fix adrenal fatigue issues before you tackle gut issues. Signs of adrenal fatigue include waking up in the middle of the night, racing thoughts, vertigo or dizziness, long recuperation time after exercise, cravings for salt and feeling extremely fatigued.

The healing process for leaky gut becomes infinitely harder if you’re not sleeping well. In fact poor sleep and burn out will only sabotage your efforts. Good news is that two of the R’s, remove and replace, are part of adrenal healing. For more information on how to fix adrenal fatigue, read Healing Adrenal Fatigue with Hashimoto’s.

Let’s Begin. The First 2 R’s

Remove: Eliminate inflammatory and gut wrenching foods. This includes gluten (indefinitely), dairy, refined sugar, vegetable and seed oils (canola, corn, safflower, sunflower, peanut, cottonseed oil, etc), processed and fried foods (anything out of a box), alcohol, corn, GMO soy. If you feel unwell after grains and legumes, eliminate them for the time being.

Replace: Replace the inflammatory foods with gut healing foods. You’ll want to include many green leafy vegetables into your diet. The good bacteria in your gut loves them. Broccoli (well cooked), Spinach, asparagus, artichokes, brussel sprouts, arugula just to name a few. Colorful vegetables like beets, carrots, radicchio contain polyphenols, sweet potatoes and all types of squashes are excellent for the gut. My favorite is roasted butternut squash. If you are sensitive to the nightshade family, avoid tomatoes, eggplant, bell peppers and white potato.

You’ll also want to include Omega 3 Fatty acids from fatty fish like salmon, mackerel and sardines. Avoid fish high in mercury. Good fats from avocado, extra virgin olive oil and coconut oil are highly beneficial. Low glycemic fruits like wild blueberries, whole apples and unripened bananas also feed good gut bacteria. Nuts and seeds can be beneficial as long as you are not sensitive to them. I had to avoid them in the beginning.  Focus on lean meat that is grass fed and antibiotic free.

Incorporate fresh raw ginger and garlic wherever you can.  I mix them with olive oil and pink salt and put it all over salads, vegetables and even salmon.  The same goes for raw leeks and onions. All are wonderful prebiotic foods that help to fix leaky gut. Fresh herbs like basil, oregano and thyme have antibacterial properties without hurting your good bacteria. Last but not least, start drinking bone broth. Plenty of it. You can make it at home or purchase it from the store or companies that deliver it fresh to your door. Here is a recipe. Bone broth is nourishing and contains building blocks to help the gut lining heal.

Leaky Gut and Hashimoto's Disease

The Second 2 R’s

RepairThis is where bioavailable, high quality supplements come into play. I feel they are essential to rebuilding your gut. You do not want to start all of them at once, the timing should be strategic. For instance, I start out with a two week course of oil of oregano to help kill any gut pathogens. It can also kill yeast overgrowth and help with SIBO. Then I work in the other supplements two at a time in the following weeks. The supplements that help fix and prevent further deterioration of leaky gut are: digestive enzymes, N-acetyl-cysteine, oil of oregano, Vitamin D3 (only if you find out you’re deficient via lab testing), Zinc, collagen peptides, Omega 3 with EPA/DHA, L-glutamine or glutathione and anti-inflammatories like curcumin.

All supplements are not created equal and I strongly encourage you not to visit your run of the mill vitamin shop with this list. Most supplements contain fillers and very little of the active compound or nutrient you need. Ultimately, you want a supplement that is bioavailable and free from wheat, dairy, nuts, GMOs, heavy metals, corn and soy. Most people with Hashimoto’s are sensitive and reactive to one or more of these fillers.

Another note is that this round of healing can get slightly pricey. I spent a little over $260 for gut healing supplements. In the end I felt that it was a small investment to make in order to get my health back. Spending thousands, or even more, for when my symptoms got even worse made no sense to me. If price is a concern, the absolute must have supplements to fix leaky gut are the digestive enzymes, glutathione/L-glutamine, collagen peptides, Omega 3 and Vitamin D3 (again, only if you are deficient).

Reinoculate: While still continuing with an anti inflammatory diet, bone broth and some of the supplements above, it’s time to reinoculate, or repopulate, the gut with good gut bacteria. Green leafy vegetables are an excellent start but you’ll need more help. That’s where a powerful probiotic comes into play. If you have SIBO or other types of gut dysbiosis, you’ll have to be careful which probiotic you take. Some probiotics contain multiple strains and you may be feeding overgrowth of certain bacteria strains in your gut. If you can’t get tested, one option is to take saccharomyces boulardii. This probiotic does not make SIBO worse according to research. You’ll want to take at least 10-50 Billion CFUs. Soil probiotics are also a good option.

Another great way to repopulate good gut bacteria is through fermented foods. Store bought pickles won’t cut it. Homemade sauerkraut (which is easy to do), pickled vegetables, kimchi are all great examples. I love to pickle cauliflower, carrots and cucumbers. Note: Avoid fermented foods if you have Histamine Intolerance. I noticed my histamine intolerance faded as I healed my gut. Then only was I able to start eating more fermented foods.

Supplements for Leaky gut

You should always contact your doctor or a medical health professional before starting a new supplement regime. If you are taking thyroid medication, be sure to space any supplements with magnesium, calcium or iron at least 4 hours away from your medication as it can affect thyroid hormone absorption. For instance, some of my approved supplements do contain magnesium stearate so be sure to take it a safe distance away.

Below are my trusted brands for how to fix leaky gut. You can find them on Amazon. You may want to avoid purchasing Vital Proteins Collagen Peptides via Amazon as the comments seem to indicate the product being sold is not the same as the original formula. Shop their website directly.

Leaky Gut Supplements found on Amazon
Leaky Gut and Hashimoto's disease

Click Here to see my trusted brands


Please feel free to leave me any questions or comments below.


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